Sorry to hear that the saga continues. Here are my thoughts....

I reread your original post and you said it felt mushy (to be expected from an empty circuit, but) and as a result, you probably had occasion to push the pedal (and the M/C's piston inward) farther than usual. And that's probably the reason for the current problem.

As you'll recall from countless (literally) posts on this forum when someone does their brakes fluid flush for the first time using the pedal method, when they've pushed the pedal down unusually far, it moves the piston into "virgin" territory of the cylinder, where crud and rust has accumulated -- this invariably destroys the integrity of the piston's seals. Now you have a M/C with an internal leak (the fluid just circulates from the pressure side of the seals back to the unpressurized side), with the moving fluid allowing the pedal to sink. Early signs of this are sometimes intermittant -- don't trust that "...the pedal seems good now...." Be sure.

As for the other part, the warning light, that could have been building since you lost fluid in one circuit. That "octopus" under the fender compares pressures in the two circuits -- an inequality pushes its piston to one side where it closes a circuit to light the dash light.
And if the M/C is still leaking internally, it could create the pressure inequality that would trigger the octopus's switch.
It usually "latches" when it's triggered (a feature of the switch), so the light will stay on subsequently.
When you're sure there are no leaks (including the M/C), or air bubbles in the lines (have you done a thorough flushing?), you could try to give the pedal a hard, fast jab! Sometimes that bounces the piston back in place.
Otherwise, you may have to crawl underneath and screw out the switch (at the center of the octopus) to let the piston self-center itself; then reinstall it.